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Merge "Added note about make_edi and flooding in ED paragraph" into release-4-6
2013-01-17
C
h
ri
s
t
o
p
h
Jun
g
hans
Merge "Added
n
o
t
e a
b
out ma
k
e
_
ed
i
and
flooding in ED
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Ch
r
istoph Junghans
Merge "use the compiler version prov
i
ded
by CMake
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Roland S
c
hulz
Merge "Mer
g
e
branch '
r
ele
a
se-4-
5
-patches' into r
e
lea
s
e
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Szilá
r
d
P
á
l
l
Merge changes I930b316c,Iea4283e0,I103648f8 into
r
ele
a
se-
4
-
6
commit
|
commitdiff
|
tree
2013-01-17
Mar
k
A
b
ra
h
am
BlueG
e
ne/Q instal
l
ation
n
o
t
e
s
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghan
s
Merg
e
"
no
t
e
t
h
e reason
f
o
r
auto-disabling G
P
U support
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Abr
a
ham
M
er
g
e "Added
m
d
p
opti
o
n
'ca
l
c-
l
a
m
bda-neighbors'
.
"
into
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
R
o
l
a
nd Sch
u
lz
Merge "clarify w
o
rding of GPU driver
-
r
elat
e
d
n
otes
.
.
.
commit
|
commitdiff
|
tree
2013-01-17
Mark Ab
r
aha
m
Fix trjconv -su
b
with
.
t
r
r files
commit
|
commitdiff
|
tree
2013-01-17
Berk Hess
fixed S
D
+B
D
integration slo
w
ing down with O
p
enMP threads
commit
|
commitdiff
|
tree
2013-01-17
Rolan
d
S
ch
u
l
z
Run re
g
ression
t
ests from build
commit
|
commitdiff
|
tree
2013-01-17
Sander Pronk
Added m
d
p op
t
ion 'calc-l
a
mbda-neighbors'
.
commit
|
commitdiff
|
tree
2013-01-17
Mark A
b
r
a
ham
Fi
n
ally move Ope
n
MM to con
t
r
i
b
commit
|
commitdiff
|
tree
2013-01-17
Rola
n
d
Schul
z
Fix confusing gmx
_
header_config
.
h includ
e
commit
|
commitdiff
|
tree
2013-01-17
Szilard Pall
don't use polling
with n
e
w dr
i
v
e
r
commit
|
commitdiff
|
tree
2013-01-17
Christoph Junghans
clean
up for
t
ra
n
name m
a
ngling
commit
|
commitdiff
|
tree
2013-01-17
Ber
k
Hess
f
i
x
e
d nbnxn hybrid mode wi
t
h
OpenMP
commit
|
commitdiff
|
tree
2013-01-17
B
erk Hess
made PME
lo
a
d
b
alanc
i
n
g
+ DD DLB
m
ore efficie
n
t
commit
|
commitdiff
|
tree
2013-01-16
C
h
ristoph J
u
nghans
Remove debug sta
t
ment
commit
|
commitdiff
|
tree
2013-01-15
M
a
r
k
A
b
raha
m
Merge "Hid nb
n
xn kernel na
m
es behin
d
a
lookup fu
n
cti
o
n
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
C
h
ristoph J
u
nghans
Merge "Added fatal erro
r
for co
n
straints
+ L-BFGS mi
n
imizer
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Christoph Jun
g
ha
n
s
Merge "disable OpenMP
w
ith all OS X gcc 4
.
2-bas
e
d compilers
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
S
a
n
der
Pronk
Merge "C
o
n
t
in
u
ation of documentation for expanded ensem
b
le
.
.
.
commit
|
commitdiff
|
tree
2013-01-15
Mark Abraham
Vel
o
city-verle
t
i
n
t
egrator
s
and
v
-rescale a
r
e
b
r
oken
commit
|
commitdiff
|
tree
2013-01-14
Carsten K
u
tzner
Esse
n
t
i
a
l d
y
namics output file
n
ow in
.
xvg
f
orm
a
t
commit
|
commitdiff
|
tree
2013-01-14
David van d
e
r
Spoel
Merge "F
i
xing trjconv -sub" into release-4-5-pat
c
hes
commit
|
commitdiff
|
tree
2013-01-14
David
v
an der Spoel
Merge "Noting that and why gmxdump -s -sy
s
i
s broken
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
R
ola
n
d S
c
hulz
M
e
rge "Fixe
s
for md-
v
v an
d
rerun"
i
nt
o
release-4
-
6
commit
|
commitdiff
|
tree
2013-01-13
Roland Sc
h
ulz
M
e
rge "fixed resett
i
n
g
states wit
h
p
arallel Verlet
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Roland Schulz
P
r
o
p
e
r
fix for copyrite cu
d
a
dep
e
ndence
commit
|
commitdiff
|
tree
2013-01-13
Michael Sh
i
rts
Fixes
f
o
r md-vv and rerun
commit
|
commitdiff
|
tree
2013-01-13
B
erk Hess
f
ixed resetti
n
g states with pa
r
allel
Verlet
scheme
commit
|
commitdiff
|
tree
2013-01-13
C
hristoph Jungh
a
ns
Merge "R
e
move u
n
used bfunc
.
h
.
" into relea
s
e-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph
J
unghan
s
Me
r
g
e "Clarified some co
m
ments & w
a
rnings
a
b
o
ut
t
hread
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Chr
i
stoph
J
unghans
Merge "Manage BlueGene/Q c
o
nfigurati
o
n
" into releas
e
-
4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Jun
g
ha
n
s
Merge
"
R
e-organi
z
e Bl
u
eGene tool
c
hain files"
into r
e
lease-4-6
commit
|
commitdiff
|
tree
2013-01-13
Christoph Junghans
Mer
g
e "C
h
anged defau
l
t
s
f
o
r bui
l
ding sha
r
ed libraries
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
M
a
rk A
b
r
a
ham
Cla
r
ified some comments &
warnings about thread pinning
commit
|
commitdiff
|
tree
2013-01-13
Roland Schul
z
Merge "pre
p
a
red the nb
n
xn code
f
or no
n
-x
8
6
S
IMD" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-13
Mark
A
b
raham
Merge "Added basic CP
U
topology i
n
formati
o
n
t
o cpuid
.
.
.
commit
|
commitdiff
|
tree
2013-01-12
Berk Hess
pre
p
ared th
e
nb
n
xn code f
o
r non-x
8
6 SIMD
commit
|
commitdiff
|
tree
2013-01-12
C
h
r
istoph Junghans
M
e
rge "Added missin
g
expo
r
t" into
r
elease-4-6
commit
|
commitdiff
|
tree
2013-01-11
Erik Li
n
dahl
Merge
"mad
e
SHAKE work aga
i
n
w
i
th particl
e
decompostion
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Roland Schulz
Merge
"time
t
he GP
U
fo
r
ce cl
e
aring async
l
aunch overhe
a
d
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Chr
i
stoph Junghans
Merge
"c
o
nsole and log
o
u
tput
improvements
"
into
r
ele
a
se-4-6
commit
|
commitdiff
|
tree
2013-01-11
Christoph Junghans
M
e
r
ge "F
i
x CUDA being
q
uie
t
and
mark all CUD
A
_* as
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Erik
Lindahl
Added basic
CPU
topology info
r
ma
t
ion to cpuid code
commit
|
commitdiff
|
tree
2013-01-11
E
r
ik Li
n
dahl
Merge "fi
x
ed
nbnxn no LJ c
o
mb
.
rule
AVX256 PM
E
kernel
.
.
.
commit
|
commitdiff
|
tree
2013-01-11
Roland Schulz
Merg
e
"Handle c
o
mpiler flags mo
r
e
f
lexibly" i
n
to relea
s
e-4
-
6
commit
|
commitdiff
|
tree
2013-01-11
Christoph J
u
nghans
Merge "Remove in
c
or
r
ect as
s
ert a
d
de
d
by 0
5
f9a740" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Berk
H
ess
fix
e
d nb
n
xn no LJ
c
o
m
b
.
rule
A
V
X
256
P
ME ke
r
nel
commit
|
commitdiff
|
tree
2013-01-10
Er
i
k Lindahl
Fixed flop-accounting
f
o
r periodic improp
e
r dihedrals
commit
|
commitdiff
|
tree
2013-01-10
Mark Abraham
Me
r
g
e
"Revert default
rl
i
st/rvdw/rcoulomb
t
o valid
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
M
ark Abraha
m
Merge "fixed bug with Verl
e
t
+
DD
+
bond
e
d ato
m
commun
i
catio
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland Schulz
Handle compil
e
r
flag
s
more fl
e
xibly
commit
|
commitdiff
|
tree
2013-01-10
Er
i
k Lindahl
D
is
a
llow the use of
C
lang to co
m
pile AVX_12
8
_FMA
commit
|
commitdiff
|
tree
2013-01-10
R
oland Schulz
Merge "Move Windo
w
s
shar
e
d/static options t
o
lat
e
r
.
.
.
commit
|
commitdiff
|
tree
2013-01-10
Roland Sc
h
ulz
Mer
g
e "Remov
e
workaround" into
release-4-6
commit
|
commitdiff
|
tree
2013-01-10
Roland Schulz
Move
Wi
n
dows sha
r
ed/static options
to later point
commit
|
commitdiff
|
tree
2013-01-10
Roland Sc
h
ulz
R
e
m
o
ve workaround
commit
|
commitdiff
|
tree
2013-01-10
Erik Lindahl
Remove broke
n
g_di
h
tool
commit
|
commitdiff
|
tree
2013-01-10
Mark
A
braham
Me
r
ge "Fixes SSE/AVX compilati
o
n
under Window
s
" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Eri
k
Li
n
dahl
Merge "Corre
c
ted gmxcheck output for
Gromos96
bonds
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland
S
c
h
ulz
M
e
r
g
e
"
Ad
d
e
d
w
o
rk-aroun
d
for gcc bug in AVX intrinsin
c
s
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Ro
l
and
S
chulz
Merge "Ad
d
check to rem
o
ve zero Charmm di
h
edra
l
s" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-09
Roland Schulz
Merge
"
[tool
s
] g_sans - add trajectory ave
r
e
ging" into
.
.
.
commit
|
commitdiff
|
tree
2013-01-08
Erik Lindahl
Add check
to remove zer
o
Charmm dihedral
s
commit
|
commitdiff
|
tree
2013-01-08
Erik Lindahl
Do not always
a
dd -
m
sse2 to release flags
for icc
commit
|
commitdiff
|
tree
2013-01-08
Roland
S
ch
u
l
z
Me
r
ge "Reduce
use of monolithic sets of compiler flags
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland
Schul
z
Mer
g
e
"fixed nbnxn AVX-256 E
w
a
l
d table poi
n
ter alignmen
t
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Mark
A
braham
R
educe use of monolithic
sets
o
f comp
i
le
r
flags
commit
|
commitdiff
|
tree
2013-01-07
Rol
a
nd Sc
h
ulz
Merge
"cmak
e
: r
e
mov
e
d
o
u
b
le-negative quotes logic"
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
M
e
r
g
e "Print out atom n
u
m
b
ers in g_rms
f
" into rel
e
ase
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
B
e
rk
Hess
fi
x
e
d nbnxn AVX-2
5
6 Ew
a
l
d t
a
ble po
i
nter ali
g
nment
commit
|
commitdiff
|
tree
2013-01-07
Roland S
c
hulz
Merge "Ignore bool cast warni
n
g
for MSVC
and C++
"
in
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Davi
d
van der S
p
oel
Merge
"Removed reference to nonexistent fil
e
i
n
g_helix
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Sc
h
u
l
z
Merge "improv
e
d
repor
t
ing of
fail
e
d
a
ffi
n
ity set
t
ing
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Rolan
d
S
ch
u
l
z
Merge
"Fixed format erro
r
in onl
i
ne manual
.
"
into release-
4
-6
commit
|
commitdiff
|
tree
2013-01-07
Roland S
c
hulz
Merg
e
"
F
i
xed a bug that with m
u
ltip
l
e ex
c
hanges"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Roland Schulz
Merge "
E
ss
e
ntial d
y
namics:
f
i
x
e
d restart
s
wh
e
n
ED group
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Rola
n
d S
c
hulz
Merge
"
minor speed-up
a
nd code clean-up in nbnxn ker
n
els
.
.
.
commit
|
commitdiff
|
tree
2013-01-07
Christo
p
h
J
u
n
g
ha
n
s
Merge "Make gmx_cp
u
id
.
h s
e
lf-standing
.
" into rele
a
se-4-6
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murtol
a
Merge "Mino
r
fixes to
g
_angle help descri
p
tion
.
"
i
n
t
o
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Ma
r
k Abrah
a
m
Set CMake mo
d
ule sear
c
h path at a bett
e
r time
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murto
l
a
Merge "add a
n
o
ption to
n
o
t
b
uild the template"
i
nto
.
.
.
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murtol
a
Merge "Add mi
s
sing
de
f
ines to P
K
G_CFLAGS" into release-4-6
commit
|
commitdiff
|
tree
2013-01-04
Teemu Murto
l
a
M
e
rge "Fixed
e
rr
o
r message for z
w
itterion
resid
u
es
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
Christoph Junghans
add an option to not
build the template
commit
|
commitdiff
|
tree
2013-01-03
Ch
r
istoph Jun
g
hans
Add missing d
e
fines to PKG_CFLAGS
commit
|
commitdiff
|
tree
2013-01-03
Roland Schulz
Merge "Fi
x
ed GMXRC so we ar
e
not
p
ollut
i
ng standard
.
.
.
commit
|
commitdiff
|
tree
2013-01-03
Christoph Junghans
Merg
e
"Remove non
-
functional Po
w
er
P
C
invsqrt
.
" in
t
o
.
.
.
commit
|
commitdiff
|
tree
2012-12-30
E
r
ik Lind
a
hl
M
erge "Thr
e
ad-MP
I
fixes for
i
386 llvm & simpli
f
icat
i
on
.
.
.
commit
|
commitdiff
|
tree
2012-12-22
A
l
e
xey Shvetsov
[tools] g_sans - add trajectory avereging
commit
|
commitdiff
|
tree
2012-12-22
Mark Abraham
New beta re
l
ea
s
e: 4
.
6-beta
3
commit
|
commitdiff
|
tree
2012-12-22
Christoph Ju
n
ghans
cmake: mark FFT
W
_HAV
E
_{
S
I
MD,AVX
}
a
s ad
v
a
nced
commit
|
commitdiff
|
tree
2012-12-22
Roland
S
chulz
Add missing visibility exports
commit
|
commitdiff
|
tree
2012-12-21
C
hrist
o
ph Junghans
Merg
e
"Remove non-functional compiler override for
.
.
.
commit
|
commitdiff
|
tree
2012-12-21
Eri
k
Li
n
dahl
Fixed gmx_cp
u
id not working
o
n
n
on-x86
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindah
l
Merge "cma
k
e
:
a
d
ded opt
i
o
n
t
o disabl
e
quot
e
s" into
.
.
.
commit
|
commitdiff
|
tree
2012-12-20
Erik Lindahl
Me
r
g
e "
S
mall
fix
for g_tune_pme" i
n
t
o
r
e
lease-4-6
commit
|
commitdiff
|
tree
next